knitr::opts_chunk$set(echo = TRUE, root.dir = here::here())

library(dplyr)
library(ggplot2)
set.seed(2019)

Bryois 2020

bryois <- readxl::read_excel(here::here("data/metaanalysis/TableS2.xlsx"), sheet="Bryois2020_corr")

mat_bryois <- as.matrix(bryois$rg) %>% `rownames<-`(bryois$Trait2) %>% `colnames<-`("rg")

heat <- ggplot(bryois, aes(y=Trait2, x=1, fill=rg)) +
  geom_tile() + 
  theme_bw()
plotly::ggplotly(heat)

LD Hub

I began to explore this dataset but then realized it does not contain any Parkinson’s Disease GWAS.

rg = xlsx::read.xlsx(here::here("data/LD_Hub/LD-Hub_genetic_correlation_221x221_no_ENIGMA.xlsx"), sheetName = "rG") %>% 
  tibble::column_to_rownames("NA.")
colnames(rg) <- gsub("[.]","-",colnames(rg))
row.names(rg) <- gsub("[.]","-",row.names(rg))
rg[rg=="/"] <- NA 
rg <- Matrix::as.matrix(rg, sparse = T)


rp = xlsx::read.xlsx(here::here("data/LD-Hub_genetic_correlation_221x221_no_ENIGMA.xlsx"), sheetName = "rP")%>%
    tibble::column_to_rownames("NA.")
colnames(rp) <- gsub("[.]","-",colnames(rp))
row.names(rp) <- gsub("[.]","-",row.names(rp))
rp[rp=="/"] <- NA 
rp <- Matrix::as.matrix(rp, sparse = T)

Check for Parkinson’s

grep("Parkinson",colnames(rp), ignore.case = T, value = T)

Session Info

utils::sessionInfo()
## R version 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] ggplot2_3.3.5 dplyr_1.0.7  
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7        cellranger_1.1.0  pillar_1.6.2      bslib_0.2.5.1    
##  [5] compiler_4.1.0    jquerylib_0.1.4   tools_4.1.0       digest_0.6.27    
##  [9] viridisLite_0.4.0 jsonlite_1.7.2    evaluate_0.14     lifecycle_1.0.0  
## [13] tibble_3.1.3      gtable_0.3.0      pkgconfig_2.0.3   rlang_0.4.11     
## [17] DBI_1.1.1         crosstalk_1.1.1   yaml_2.2.1        xfun_0.25        
## [21] httr_1.4.2        withr_2.4.2       stringr_1.4.0     knitr_1.33       
## [25] htmlwidgets_1.5.3 generics_0.1.0    vctrs_0.3.8       sass_0.4.0       
## [29] rprojroot_2.0.2   grid_4.1.0        tidyselect_1.1.1  data.table_1.14.0
## [33] glue_1.4.2        here_1.0.1        R6_2.5.0          plotly_4.9.4.9000
## [37] fansi_0.5.0       readxl_1.3.1      rmarkdown_2.10    farver_2.1.0     
## [41] tidyr_1.1.3       purrr_0.3.4       magrittr_2.0.1    scales_1.1.1     
## [45] ellipsis_0.3.2    htmltools_0.5.1.1 assertthat_0.2.1  colorspace_2.0-2 
## [49] labeling_0.4.2    utf8_1.2.2        stringi_1.7.3     lazyeval_0.2.2   
## [53] munsell_0.5.0     crayon_1.4.1